I've played the Pathogen-X demo, and I was blown away by its combination of OTS horror a la Dead Space and RE4, and traditional oldschool Survival Horror a la Resident Evil 1 - Zero and the Outbreak spin-offs.
But for the story, I'd like to ask a few suggestions for a compelling narrative:
#1 Make the regular enemies Zombies. I'm mainly asking this out of spite for the ever-growing dirge of generic action games about uber-badass warriors beating the crap out of them, so I'd really like a game that makes Zombies scary again. The hookmen can work as elite-type enemies, who both take and deal more damage.
#2 Have a unique explanation. The whole 'Science did it' thing has been done to death, so why not try something new? Maybe have it be so that the titular Pathogen is actually a voodoo disease or something.
#3 A Scientist hero. Hawk works as the protagonist of the Arcade mode, but for the main story, you need a truly memorable protagonist who can match wits with the best of them (Leon S. Kennedy, Harry Mason, Isaac Clarke, etc.). I think a Scientist as the main character could put a new spin on traditional survival horror storytelling. If we have countless tales of soldiers in peril, why not break away from that?
And that's all I have. Maybe you'd like these suggestions, maybe not, but no matter what, here's hoping you have an entertaining horror yarn for your game!